AMBER Archive (2005)

Subject: Re: AMBER: Replica-Exchange MD from AMBER8!

From: Peng Tao (amberhelp_at_gmail.com)
Date: Sat Dec 03 2005 - 14:19:12 CST

Dr. Carlos Simmerling,

There is one more strange thing I just noted.

In the command line to run sander, the initial coordinate of the system is
given by inpcrd file, and restart file will be saved to restrt file.

But something strange happened to my REMD run with two replicas.

My two INPCRD files are md.r.000 and md.r.001 without temperature. But it
seemed that these two INPCRD files have not been used for two REMD replicas.

Here are what I got in sander output files.

The head of pre-md run output file rem.out:
///////////////////////////////////////////////////////////////////

          -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------

| Run on 12/03/2005 at 15:00:48
  [-O]verwriting output

File Assignments:
| MDIN: rem.in.000

| MDOUT: rem.out

|INPCRD: md.r.000

| PARM:
prmtop
|RESTRT: rem.rstrt.000

| REFC:
refc
| MDVEL:
mdvel
| MDEN: mden.000

| MDCRD: rem.traj

|MDINFO: rem.mdinfo

|INPDIP:
inpdip
|RSTDIP:
rstdip

 Here is the input file:

md9.in - PyrFurDuplex gb test run, igb =
1
 &cntrl

  imin = 0, nstlim = 5000, dt = 0.002,

 ntx = 5, tempi = 0.0, temp0 = 267.0,

 ntt = 1, tol = 0.000001, saltcon = 0.2,

 ntc = 2, ntf = 1, ntb = 0, nsnb =
20,
 ntwx = 10, ntwe = 0, ntwr = 500, ntpr =
500,
 scee = 1.2, cut = 99.0,

 ntr = 0, tautp = 0.1, offset = 0.09,

 nscm = 500, igb = 1, numexchg =
2,
 irest = 1, ntave =
0,
/

///////////////////////////////////////////////////////////////////

In this run, md.r.000 has been used as INPCRD file. And rem.rstrt.000 is
output file.

In one replica run, the output file rem.out.000 has head

//////////////////////////////////////////////////////////////////

          -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------

| Run on 12/03/2005 at 15:01:43
  [-O]verwriting output

File Assignments:
| MDIN: rem.in.000

| MDOUT: rem.out.000

|INPCRD: rem.rstrt.000

| PARM:
prmtop
|RESTRT: rem.rstrt.000

| REFC:
refc
| MDVEL:
mdvel
| MDEN: mden.000

| MDCRD: rem.traj.000

|MDINFO: rem.mdinfo.000

|INPDIP:
inpdip
|RSTDIP:
rstdip

 Here is the input file:

md9.in - PyrFurDuplex gb test run, igb =
1
 &cntrl

  imin = 0, nstlim = 5000, dt = 0.002,

 ntx = 5, tempi = 0.0, temp0 = 267.0,

 ntt = 1, tol = 0.000001, saltcon = 0.2,

 ntc = 2, ntf = 1, ntb = 0, nsnb =
20,
 ntwx = 10, ntwe = 0, ntwr = 500, ntpr =
500,
 scee = 1.2, cut = 99.0,

 ntr = 0, tautp = 0.1, offset = 0.09,

 nscm = 500, igb = 1, numexchg =
2,
 irest = 1, ntave =
0,
/

///////////////////////////////////////////////////////////////////

In this run, rem.rstrt.000 is INPCRD file, and again, rem.rstrt.000 is also
RESTRT file. I am confused by this, because I thought md.r.000 is suposed to
be INPCRD for this run.

In another run, output file rem.out.001 has head as

///////////////////////////////////////////////////////////////////

          -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------

| Run on 12/03/2005 at 15:01:43
  [-O]verwriting output

File Assignments:
| MDIN: rem.in.001

| MDOUT: rem.out.001

|INPCRD: rem.rstrt.001

| PARM:
prmtop
|RESTRT: rem.rstrt.001

| REFC:
refc
| MDVEL:
mdvel
| MDEN: mden.001

| MDCRD: rem.traj.001

|MDINFO: rem.mdinfo.001

|INPDIP:
inpdip
|RSTDIP:
rstdip

 Here is the input file:

md9.in - PyrFurDuplex gb test run, igb =
1
 &cntrl

  imin = 0, nstlim = 5000, dt = 0.002,

 ntx = 5, tempi = 0.0, temp0 = 289.0,

 ntt = 1, tol = 0.000001, saltcon = 0.2,

 ntc = 2, ntf = 1, ntb = 0, nsnb =
20,
 ntwx = 10, ntwe = 0, ntwr = 500, ntpr =
500,
 scee = 1.2, cut = 99.0,

 ntr = 0, tautp = 0.1, offset = 0.09,

 nscm = 500, igb = 1, numexchg =
2,
 irest = 1, ntave =
0,
/

///////////////////////////////////////////////////////////////////

Again, rem.rstrt.001 is both INPCRD and RESTRT file. The other INPCRD file
md.r.001 seemed not be used at all in the REMD simulation.

Did I messed up some input files again?

The PBS setup file:

///////////////////////////////////////////////////////////////////

#PBS -N olig8HelRGBREMDtest.in
#PBS -l mem=50mw
#PBS -l walltime=533
#PBS -l nodes=2:ppn=1
#PBS -j oe
#PBS -m ae
#PBS -S /bin/csh

module load amber
setenv AMBERHOME /usr/local/amber/amber8

set
WORKDIR=/a/osu3112/work/crc/project1/oligomer/gbmd/oligomer8/helixR/run05REMDtest

#cd
/a/osu3112/work/crc/project1/oligomer/gbmd/oligomer8/helixR/run05REMDtest

#cd $TMPDIR

#cp $WORKDIR/* .

cd $WORKDIR

set MDIN=rem.in
set MDOUT=rem.out
set MDEN=rem.mden
set MDVEL=rem.mevel
set MDINFO=rem.mdinfo
set PRMTOP=prmtop
set INPCRD=md.r
set TRAJ=rem.traj
set RESTRT=rem.rstrt

mpiexec /usr/local/amber/amber8/exe/sander.REM -O -ng 2 -rem 1 -remlog
olig8HelRGBREMD.log -i $MDIN -o $MDOUT -inf $MDINFO -p $PRMTOP -x $TRAJ -c
$INPCRD -r $RESTRT

#cp * $WORKDIR

ls -al
pwd

///////////////////////////////////////////////////////////////////
By the way, two restart file rem.restrt.000 and rem.restrt.001 weren't there
at all.

I also attached all the files except three large trajectory files.

Thanks again for your help.

Best regards,
Peng Tao

On 12/2/05, Carlos Simmerling <carlos.simmerling_at_stonybrook.edu> wrote:
>
> I think that one problem is that both of your inpcrd files
> (rem.rstrt.00X) have
> a temperature of 300K in the header. In REMD, the temp0 values is
> placed in the restart file for reading in the next MD step. These will
> override any value in the mdin. So, delete the third number on the
> second line of
> the restarts and try again.
>
> amber9 will have bettter error checking of this sort of thing- but with
> amber8, if 2 replicas are at the same T it can cause problems with
> the exchange calculation.
>
> try this fix and let me know if it still behaves strangely.
> carlos
>
> Peng Tao wrote:
>
> > Dear all,
> >
> >
> > I am trying to use REMD from AMBER8, but I have some problem to use
> > this program.
> >
> > First I run the examples of REMD downloaded from AMBER home page
> > (amber.scripps.edu <http://amber.scripps.edu>)
> > Replica exchange (REM) test suite for Amber 8:
> > http://amber.scripps.edu/amber8.remtests.tar.gz
> >
> > I used rem_gbrun example, because I am using GB model in my current
> > research.
> >
> > Fortunately, I can run this test successfully. That means, when I
> > tried to run REMD with two replicas, I got three output files:
> >
> > rem.out rem.out.000 and rem.out.001
> >
> > three mdinfo files:
> >
> > rem.mdinfo rem.mdinfo.000 and rem.mdinfo.001
> >
> > three trajectory files:
> >
> > md.traj md.traj.000 and md.traj.001
> >
> > and two restart fiels:
> >
> > rem.rstrt.000 and rem.rstrt.001
> >
> >
> >
> > Unfortunately, when I tried to run my own examples, I got problems.
> >
> > My system is a small dendron molecule. I built it by XLEaP.
> >
> > It seemed that AMBER8 REMD can run MD for this system, but several
> things
> > went wrong here.
> >
> > 1) I tried to run REMD with two replicas. But instead of three, I got
> only
> > two MD run results.
> >
> >
> >
> > Here are what I have:
> >
> > One topology file: prmtop
> >
> > two sander input file: rem.in.000 and rem.in.001
> >
> > two cordinates file: rem.r.000 and rem.r.001
> >
> > One PBS job file: olig8HelRGBREMD.Job
> >
> >
> > Here are what I got:
> >
> > Two output files: rem.out and rem.out.000
> > (I missed one more output file rem.out.001 here)
> >
> > Two trajectory files: rem.traj and rem.traj.000
> > (I missed one more trajecotry file rem.traj.001 here)
> >
> > Two mdinfo files: rem.mdinfo and rem.mdinfo.000
> > (I missed one more mdinfo file rem.mdinfo.001 here)
> >
> > Two restart files: rem.rstrt.000 and rem.rstrt.001
> > (But I have rem.rstrt.001 here)
> >
> >
> >
> > 2) In rem.out.000, I found input setup for this MD run is:
> > //////////////////////////////////////////////
> > File Assignments:
> > | MDIN: rem.in.001
> > | MDOUT: rem.out.000
> > |INPCRD: rem.rstrt.001
> > | PARM: prmtop
> > |RESTRT: rem.rstrt.001
> > | REFC: refc
> > | MDVEL: mdvel
> > | MDEN: mden.001
> > | MDCRD: rem.traj.000
> > |MDINFO: rem.mdinfo.000
> > |INPDIP: inpdip
> > |RSTDIP: rstdip
> > /////////////////////////////////////////////
> >
> > I really cannot understand why REMD use rem.in.001 for this run,
> > and still set output file with 000 extension.
> >
> >
> > 3) In olig8HelRGBREMD.log, two exchanges occurred. But both Temp0 and
> > NewTemp0 are 300.00K. However, in rem.in.000, I setup temp0 as 267.0 K,
> in
> > rem.in.001, I setup temp0 as 289.0 K. I didn't know where did sander get
> > 300.00 K as temp0.
> >
> > Here are my input and output files:
> >
> > olig8HelRGBREMD.Job:
> >
> > //////////////////////////////////////////////////////
> >
> > #PBS -N olig8HelRGBREMDtest.in
> > #PBS -l mem=50mw
> > #PBS -l walltime=933
> > #PBS -l nodes=2:ppn=1
> > #PBS -j oe
> > #PBS -m ae
> > #PBS -S /bin/csh
> >
> >
> > module load amber
> > setenv AMBERHOME /usr/local/amber/amber8
> >
> > cd /a/osu3112/work/test/amber8REMDbug/rem_gbrun05
> >
> >
> > set MDIN=rem.in <http://rem.in>
> > set MDOUT=rem.out
> > set MDINFO=rem.mdinfo
> > set PRMTOP=prmtop
> > set INPCRD=rem.r
> > set TRAJ=rem.traj
> > set RESTRT=rem.rstrt
> >
> > mpiexec /usr/local/amber/amber8/exe/sander.REM -O -ng 2 -rem 1
> > -remlog olig8HelRGBREMD.log -i $MDIN -o $MDOUT -inf $MDINFO -p
> > $PRMTOP -x $TRAJ -c $INPCRD -r $RESTRT
> >
> > //////////////////////////////////////////////////////
> >
> > rem.in.000:
> >
> > //////////////////////////////////////////////////////
> >
> > md9.in <http://md9.in> - PyrFurDuplex gb test run, igb = 1
> > &cntrl
> > imin = 0, nstlim = 5000, dt = 0.002,
> > ntx = 5, tempi = 0.0, temp0 = 267.0,
> > ntt = 1, tol = 0.000001, saltcon = 0.2,
> > ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
> > ntwx = 10, ntwe = 0, ntwr = 500, ntpr = 500,
> > scee = 1.2, cut = 99.0,
> > ntr = 0, tautp = 0.1, offset = 0.09,
> > nscm = 500, igb = 1, numexchg = 2,
> > irest = 1, ntave = 0,
> > /
> > //////////////////////////////////////////////////////
> >
> >
> >
> > rem.in.001:
> >
> > //////////////////////////////////////////////////////
> >
> > md9.in <http://md9.in> - PyrFurDuplex gb test run, igb = 1
> > &cntrl
> > imin = 0, nstlim = 5000, dt = 0.002,
> > ntx = 5, tempi = 0.0, temp0 = 289.0,
> > ntt = 1, tol = 0.000001, saltcon = 0.2,
> > ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
> > ntwx = 10, ntwe = 0, ntwr = 500, ntpr = 500,
> > scee = 1.2, cut = 99.0,
> > ntr = 0, tautp = 0.1, offset = 0.09,
> > nscm = 500, igb = 1, numexchg = 2,
> > irest = 1, ntave = 0,
> > /
> > //////////////////////////////////////////////////////
> >
> >
> >
> > Output file by PBS
> >
> > //////////////////////////////////////////////////////
> >
> > RUNNING MULTISANDER VERSION OF SANDER AMBER8
> > Total processors = 2
> > Number of groups = 2
> >
> > Looping over processors:
> > WorldRank is the global PE rank
> > NodeID is the local PE rank in current group
> >
> > Group = 0
> > WorldRank = 0
> > NodeID = 0
> >
> > Group = 1
> > WorldRank = 1
> > NodeID = 0
> >
> > //////////////////////////////////////////////////////
> >
> >
> >
> > Head of one output file rem.out:
> >
> > //////////////////////////////////////////////////////
> >
> >
> > -------------------------------------------------------
> > Amber 8 SANDER Scripps/UCSF 2004
> > -------------------------------------------------------
> >
> > | Run on 12/02/2005 at 14:24:03
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: rem.in.000
> > | MDOUT: rem.out
> > |INPCRD: rem.r.000
> > | PARM: prmtop
> > |RESTRT: rem.rstrt.000
> > | REFC: refc
> > | MDVEL: mdvel
> > | MDEN: mden.000
> > | MDCRD: rem.traj
> > |MDINFO: rem.mdinfo
> > |INPDIP: inpdip
> > |RSTDIP: rstdip
> >
> >
> > Here is the input file:
> >
> > md9.in <http://md9.in> - PyrFurDuplex gb test run, igb = 1
> > &cntrl
> > imin = 0, nstlim = 5000, dt = 0.002,
> > ntx = 5, tempi = 0.0, temp0 = 267.0,
> > ntt = 1, tol = 0.000001, saltcon = 0.2,
> > ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
> > ntwx = 10, ntwe = 0, ntwr = 500, ntpr = 500,
> > scee = 1.2, cut = 99.0,
> > ntr = 0, tautp = 0.1, offset = 0.09,
> > nscm = 500, igb = 1, numexchg = 2,
> > irest = 1, ntave = 0,
> > /
> >
> > //////////////////////////////////////////////////////
> >
> >
> >
> >
> >
> > Head of one output file rem.out.000:
> >
> > //////////////////////////////////////////////////////
> >
> > -------------------------------------------------------
> > Amber 8 SANDER Scripps/UCSF 2004
> > -------------------------------------------------------
> >
> > | Run on 12/02/2005 at 14:25:02
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: rem.in.001
> > | MDOUT: rem.out.000
> > |INPCRD: rem.rstrt.001
> > | PARM: prmtop
> > |RESTRT: rem.rstrt.001
> > | REFC: refc
> > | MDVEL: mdvel
> > | MDEN: mden.001
> > | MDCRD: rem.traj.000
> > |MDINFO: rem.mdinfo.000
> > |INPDIP: inpdip
> > |RSTDIP: rstdip
> >
> >
> > Here is the input file:
> >
> > md9.in <http://md9.in> - PyrFurDuplex gb test run, igb = 1
> > &cntrl
> > imin = 0, nstlim = 5000, dt = 0.002,
> > ntx = 5, tempi = 0.0, temp0 = 289.0,
> > ntt = 1, tol = 0.000001, saltcon = 0.2,
> > ntc = 2, ntf = 1, ntb = 0, nsnb = 20,
> > ntwx = 10, ntwe = 0, ntwr = 500, ntpr = 500,
> > scee = 1.2, cut = 99.0,
> > ntr = 0, tautp = 0.1, offset = 0.09,
> > nscm = 500, igb = 1, numexchg = 2,
> > irest = 1, ntave = 0,
> > /
> >
> > //////////////////////////////////////////////////////
> >
> >
> >
> > REMD log file:
> >
> > //////////////////////////////////////////////////////
> >
> > # replica exchange log file
> > # Replica #, Velocity Scaling Factor, T, Eptot, Temp0, NewTemp0
> > # exchange 1
> > 1 1.00 315.94 80.49 300.00 300.00
> > 2 1.00 306.34 89.22 300.00 300.00
> > # exchange 2
> > 1 1.00 292.12 88.27 300.00 300.00
> > 2 1.00 319.21 79.67 300.00 300.00
> > //////////////////////////////////////////////////////
> >
> >
> >
> > I also put all my REMD run related files in the attachment
> > remdrun.tar.gz except two trojectory files.
> >
> > Thank you so much in advance for help.
> >
> >
> > Best regards,
> > Peng Tao
> >
> >
> >
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu